External Email - Use Caution Dear Doug,
Thank you for your help. On the query on atlas, We have a atlas that was built at our institute comprising of 183 regions and these 183 regions are available each as a nifti file with the probability information of finding the structure at that location. I would like to build that atlas in freesurfer and use it for our analyses. On reading your documentation, I found that we have to load in each subject, draw its labels and build the atlas. I would like to know if we have a way where we can use these probability information directly and create the atlas. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Wednesday, May 2, 2018 11:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Query regarding creation of atlas directly from probabilistic information For vol2surf, you should make sure that the registration is correct by running tkregisterfv --mov ID076_LL_PHGa_l_HvOx_prob.mgz --reg $FREESURFER_HOME/average/mni152.register.dat --surfs You ROI should be in the right spot and the surface should cut through it (or near enough given your projection). If those are probabilities, then you will need to binarize it (mri_binarize) before running mri_cor2label Not sure about your other question. Do you want to get the probabilities for the DK atlas? On 05/02/2018 10:26 AM, Mageshwar Selvakumar wrote: > > Dear Everyone, > > A kind reminder. I'm unable to look beyond this step and am really > looking for some help. I would like to know if we can use the > probabilistic information directly on mri_train > > Thank you, > > Kind regards > > Mageshwar Selvakumar, M.Sc > > Department of Pharmakologische Bildgebung und Bildanalyse > > Friedrich Alexander Universität Erlangen Nürnberg > > > Office:Fahrstr. 17, 91054 Erlangen > > Phone:+ 49-9131-8522898 > > > > ------------------------------------------------------------------------ > *From:* Mageshwar Selvakumar <mageshwar.selvaku...@outlook.com> > *Sent:* Monday, April 23, 2018 10:36 AM > *To:* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl > *Subject:* Query regarding creation of atlas directly from > probabilistic information > Dear All and Bruce, > > This mail is on top of the query I had a couple of weeks back where I > misinterpreted that I had binary mask of each structure > as individual nifti volume files but on closer look, the nifti files > had the probability that the structure is present at that certain > location. On looking into the freesurfer website, I came across this > documentation of creation of Atlas, > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas > SurfaceLabelAtlas - Free Surfer Wiki > <https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas> > Overview. This document provides an overview of two related topics: > How the FreeSurfer pipeline automatically labels a subject's regions > (producing an annotation file) by comparing the subject's curvature > data to an "atlas" ("gcs") file. > surfer.nmr.mgh.harvard.edu > > In this documentation the process is done by looping through N > subjects to get the probability information, and these subjects are > registered to the registration template derived from average of > reference templates. I would like to know if I could use these > probability information directly and since the atlas information is > already in the MNI152 space, can I use the registration template which > is already available with freesurfer, and if yes, can someone guide me > on which registration files I must use. > > Secondly, I tried using mri_vol2surf and tried to convert the volume > data to a surface data before creating labels, but on doing so I had > errors when creating labels from the surface files. > To convert into volume I ran the below code: > > > *mri_vol2surf --mov ID076_LL_PHGa_l_HvOx_prob.mgz --ref > ID076_LL_PHGa_l_HvOx_prob.mgz --out > ID076_LL_PHGa_l_HvOx_prob_surf.mgz --hemi lh --mni152reg > --projdist-max -2 0 .1 --reshape --interp nearest* > > > Then I to convert this surface file into label I ran > > *mri_cor2label --i ID080_CPuP_l_HvOx_prob_surf.mgz --l area1.label > --id 076* > > > And I got the error > > *Found 0 label voxels > > ERROR: found no voxels matching id 76* > > > But the process runs fine if I run the mri_cor2label on the volume > file. It would be nice if someone can help me out on where I'm going > wrong here. > > Thank you, > > Kind regards > > Mageshwar Selvakumar, M.Sc > > Department of Pharmakologische Bildgebung und Bildanalyse > > Friedrich Alexander Universität Erlangen Nürnberg > > > Office:Fahrstr. 17, 91054 Erlangen > > Phone:+ 49-9131-8522898 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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